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United States Department of Agriculture

Agricultural Research Service

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Research Project: NOVEL SNP DISCOVERY AND GENOME ASSEMBLY OF WATER BUFFALO

Location: Animal Genomics and Improvement Laboratory

2012 Annual Report


1a.Objectives (from AD-416):
ARS and the Cooperator (The International Water Buffalo Consortium, represented by Parco Tecnologico Padano [PTP] as coordinator and The Department of Animal Science University of Tuscia [UniTus] as administrative center) are interested in developing a first draft sequence assembly of the water buffalo genome based on the bovine species, Bubalis bubalis, which encompasses the prototypical beef and dairy animal in South Asian, Brazilian and Italian production environments. Such a resource is essential for developing informative SNP markers to intensify outputs in current production scenarios and enable selection of locally-adapted breeds in developing-world water buffalo populations. Our Project Plan has two objectives: .
1)generate a 33X genome sequence coverage of DNA sequence from an Italian inbred female to use in building a genome sequence assembly and.
2)generate additional sequence coverage from additional animals to identify SNP for development of a high density SNP assay that contains informative SNP for all breed types of water buffalo. The Cooperator has the funding and genomic DNA material to properly initiate this project, and the expertise and knowledge of the water buffalo production systems to extend application of the results to improve production. ARS has the expertise and facilities to generate the DNA sequence information on next-generation sequencing platforms and characterize the SNP that are potentially informative across all breeds of water buffalo.


1b.Approach (from AD-416):
The project will be managed jointly between ARS and the Cooperator. The Cooperator will evaluate the Water Buffalo herdbook in Italy to guide collection of tissues and/or DNA material from an appropriate buffalo for sequencing. The Cooperator will then provide genomic DNA templates from this animal along with funding to purchase reagents that will generate more than 33X genome equivalent coverage of DNA sequence. ARS will generate the DNA libraries, and provide next-generation DNA sequencing services to generate at least 33X genome coverage of sequence at cost with a small amount for the overhead costs of instrumentation. ARS will analyze, store, and distribute sequence information (as agreed upon with the Cooperator) that will be used for both genome assembly and SNP discovery. Identification of SNP for marker development will be carried out collaboratively by ARS and the Cooperator. Both ARS and the Cooperator will jointly aid development of the genome assembly led by outside parties that possess the necessary advanced expertise for this process. The Cooperator will provide some annotation expertise prepare the data and lead the development of the publication.

All of these activities will be considered true collaborations and thus, by definition, each party will be considered to have provided a true intellectual contribution consistent with authorship.


3.Progress Report:

This project is being conducted under funding received from the International Water Buffalo Consortium being led by Parco Tecnologico Padano in Lodi and funded by University of Tuscia, Milan.

All ARS objectives were completed and a draft genome assembly of Buffalo (1.0) was produced from 81X genome coverage by non-funded partners from the University of Maryland, which is available for use upon request. The final genome assembly and annotation are still in progress, which rely on non-funded partners from the University of Maryland for completion. It should be noted that some sequence production contribution and experimental planning were derived from USMARC (Clay Center, NE). Objective 2 was completed by generating 1.2 terabases of sequence from 68 animals from various buffalo breeds collected from many different international partners in the consortium. This included a deep-sequencing coverage of swamp buffalo for comparative genome analysis. This research supported two objectives of its related in-house project: .
1)to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (obj. #1), and.
2)to use genotypic data to enhance genetic improvement through development and implementation of whole-genome selection and enhanced parentage verification approaches (obj. #2).


Last Modified: 8/29/2014
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